I hate to necropost, but as a long time woodworker and furniture builder I wanted to provide a few insights about the nature of wood and the best ways to assemble something of this nature.
Please not, I'm to trying o come across as having all the ansawers, a jerk, or a know it all. But there are several principles of woodwrkering that could be observed to greatly enhance the beauty and overal durability of these windows.
First things first. Pine while it may be about half the price of cedar will not wear as well, is not period, and is a poor choice for exterior fixtures. Cedar is a closed pore wood and will wear far, far, far better than pine. even painted.
Secondly a but joint is one of the weakest joints you can make. End grain wood is very poor at gluing and lacks the strength to last more than a few years. at best. Long grain joints provide the strongst joint and the most available gluing surface.
A good choice for a joint to replace the butt joint would be the bridle joint. It creates a set of fingers on one piece, and a single finger on the other. This provides lots of long grain surface for glue to grab onto, and is easy to cut on a router or table saw. Additionally it is the preferred joint of the original builders.
The more complex joint which is arguably the best is the mortise and tenon joint. A finger and pocket arrangement milled into the wood provides structural rigidity as well as good surface area for glue up.
Either of these joints would lend them self well to pinning which provides a mechanical retention of the joint if the glue were to fail.
If you are going to use dowels. use a dowel that is wider. a 3/4" thick board should receive a dowel 3/8 in diameter. Typically try for a 50/50 split between dowel thickness and stock thickness. You could even go 1/2 and not compromise structural strength. Just remember, dowels and biscuits are more of an alignment method and much less for structural strength.
So, in the end I hope you take the knowledge I'm offering as just that. knowledge. As I said I'm not trying to come off as preachy, just trying to inform that there are better way to build something if it is indented to last.
Price, Quality, Service... Pick any two.